Computational protocol: Vaccination of piglets at 2 and 3 weeks of age with Ingelvac PRRSFLEX® EU provides protection against heterologous field challenge in the face of homologous maternally derived antibodies

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Protocol publication

[…] Serum samples tested positive by qPCR and that exceeded a virus concentration of 3.0 GE/ml were selected for ORF5 sequence analysis. Sequencing of ORF5 was done by amplifying the respective region of the PRRSV genome by PCR directly from the samples, followed by Sanger-sequencing of the purified PCR product according to Balka et al. []. The sequencing data obtained was aligned with ORF5 sequences of PRRSV reference strains (i.e. wild type strain circulation on the farm, vaccine strains of commercially available vaccines used on the farm) and subsequent calculation of sequence similarities between the sequences. Sequence analysis was done with CLC Main Workbench v4.1.1.Phylogenetic analyses were performed using the CLUSTAL X 1.81 software employing IUB DNA weight matrix with 0.5 transition ratio. Bootstrap resampling was carried out on 100 replicate data sets. Phylogenetic trees were plotted with the TREEVIEW (Win32 version 106 1.6.6.) software. […]

Pipeline specifications

Software tools CLC Main Workbench, Clustal W, TreeViewX
Application Phylogenetics
Organisms Porcine reproductive and respiratory syndrome virus
Diseases Porcine Reproductive and Respiratory Syndrome